Hi Mary & Shayla

I have now uploaded these changes to CONN's development version (this can be downloaded from github.com/alfnie/conn; see or https://web.conn-toolbox.org/resources/c... for details). When entering multiple anatomical files per subject CONN will now automatically force functional preprocessing steps to run separately across runs in order to accommodate possible anatomical differences between runs (so you should be able to run the standard pipelines normally wihtout having to do anything differently). If you have a chance to try out the new functionality please let me know if everything works correctly and/or if you run into any issues.

Best

Alfonso

Originally posted by Mary Newsome:

Thank you, Alfonso! I see how having one mean would make sense when all of the runs were collected at the same time and not expected to be different. I had an experience similar to that of Shayla's. For an intervention design, I think both of your ideas would help a lot. (The only thought I had about where to offer the option was what if in the rare occasion that the same T1 had to be used for both sessions for some reason (e.g., corrupted or accidentally not acquired), but then one could always copy the file and have it loaded in for each subject?) 

Also, thanks picking up on that error. Thankfully, we did catch that earlier.

All the best,

Mary